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Conserved domains on  [gi|15226943|ref|NP_180440|]
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Histone superfamily protein [Arabidopsis thaliana]

Protein Classification

histone H2B family protein( domain architecture ID 19223400)

histone H2B is one of 4 core histone proteins, H2A, H2B, H3 and H4 to form the nucleosome core particle

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0005634|GO:0000786|GO:0046982|GO:0044877|GO:0030527

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 61-149 1.03e-58

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


:

Pssm-ID: 467035  Cd Length: 94  Bit Score: 176.94  E-value: 1.03e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943  61 TETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSE 140
Cdd:cd22910   6 KESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSE 85


                ....*....
gi 15226943 141 GTKAVTKFT 149
Cdd:cd22910  86 GTKAVTKYT 94
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 61-149 1.03e-58

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 176.94  E-value: 1.03e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943  61 TETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSE 140
Cdd:cd22910   6 KESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSE 85


                ....*....
gi 15226943 141 GTKAVTKFT 149
Cdd:cd22910  86 GTKAVTKYT 94
H2B smart00427
Histone H2B;
62-150 9.12e-52

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 159.60  E-value: 9.12e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943     62 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 141
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88


                   ....*....
gi 15226943    142 TKAVTKFTS 150
Cdd:smart00427  89 TKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 24-151 1.84e-49

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 154.46  E-value: 1.84e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943   24 KVAEKAPAEKKPKAGKKLPKEAvtggvekkkkrvkkSTETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQE 103
Cdd:PLN00158   3 KTPSKKPAKKAAKGAKKKGSKS--------------KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATE 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15226943  104 ASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 151
Cdd:PLN00158  69 AGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-128 1.59e-17

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 73.62  E-value: 1.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943     1 MAPKAGKKPAEKKPaekaPAEEEKVAEKAPAEKKPKAGKKLPKEAvtGGVEKKKKRVKKSTETYKIYIFKVLKQVHP--- 77
Cdd:pfam00125   1 MARNKNKANPRRGG----TAPEKKISQKSSSSSKKKTRRYRPGTV--ALKEIRKYQSSTDLLIYKLPFARVVREVVQstk 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15226943    78 -DIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLV 128
Cdd:pfam00125  75 tDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 61-149 1.03e-58

histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 176.94  E-value: 1.03e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943  61 TETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSE 140
Cdd:cd22910   6 KESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAKHAVSE 85


                ....*....
gi 15226943 141 GTKAVTKFT 149
Cdd:cd22910  86 GTKAVTKYT 94
H2B smart00427
Histone H2B;
62-150 9.12e-52

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 159.60  E-value: 9.12e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943     62 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 141
Cdd:smart00427   9 ETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 88


                   ....*....
gi 15226943    142 TKAVTKFTS 150
Cdd:smart00427  89 TKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 24-151 1.84e-49

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 154.46  E-value: 1.84e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943   24 KVAEKAPAEKKPKAGKKLPKEAvtggvekkkkrvkkSTETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQE 103
Cdd:PLN00158   3 KTPSKKPAKKAAKGAKKKGSKS--------------KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATE 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15226943  104 ASKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 151
Cdd:PLN00158  69 AGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
PTZ00463 PTZ00463
histone H2B; Provisional
 33-150 7.80e-37

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 122.59  E-value: 7.80e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943   33 KKPKAGKKlpkeaVTGGVEKKKKRVKKSTETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNK 112
Cdd:PTZ00463   4 KKPAKAKK-----AATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTR 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 15226943  113 KPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 150
Cdd:PTZ00463  79 RDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-128 1.59e-17

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 73.62  E-value: 1.59e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15226943     1 MAPKAGKKPAEKKPaekaPAEEEKVAEKAPAEKKPKAGKKLPKEAvtGGVEKKKKRVKKSTETYKIYIFKVLKQVHP--- 77
Cdd:pfam00125   1 MARNKNKANPRRGG----TAPEKKISQKSSSSSKKKTRRYRPGTV--ALKEIRKYQSSTDLLIYKLPFARVVREVVQstk 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 15226943    78 -DIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLV 128
Cdd:pfam00125  75 tDLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 70-126 1.38e-03

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 35.27  E-value: 1.38e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15226943  70 KVLKQVHPDiGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVR 126
Cdd:cd00076   8 RILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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